July 7, 2019  |  

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community.

Authors: Saha, Surya and Hosmani, Prashant S and Villalobos-Ayala, Krystal and Miller, Sherry and Shippy, Teresa and Flores, Mirella and Rosendale, Andrew and Cordola, Chris and Bell, Tracey and Mann, Hannah and DeAvila, Gabe and DeAvila, Daniel and Moore, Zachary and Buller, Kyle and Ciolkevich, Kathryn and Nandyal, Samantha and Mahoney, Robert and Van Voorhis, Joshua and Dunlevy, Megan and Farrow, David and Hunter, David and Morgan, Taylar and Shore, Kayla and Guzman, Victoria and Izsak, Allison and Dixon, Danielle E and Cridge, Andrew and Cano, Liliana and Cao, Xiaolong and Jiang, Haobo and Leng, Nan and Johnson, Shannon and Cantarel, Brandi L and Richards, Stephen and English, Adam and Shatters, Robert G and Childers, Chris and Chen, Mei-Ju and Hunter, Wayne and Cilia, Michelle and Mueller, Lukas A and Munoz-Torres, Monica and Nelson, David and Poelchau, Monica F and Benoit, Joshua B and Wiersma-Koch, Helen and D'Elia, Tom and Brown, Susan J

The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models.

Journal: Database
DOI: 10.1093/database/bax032
Year: 2017

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